Variant report

Variant	rs7828067
Chromosome Location	chr8:117796195-117796196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:117795253..117798191-chr8:117798844..117800835,2	MCF-7	breast:
2	chr8:117784066..117787028-chr8:117794164..117796661,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10109976	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10505288	0.80[AFR][1000 genomes]
rs1550856	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.90[ASN][1000 genomes]
rs16888695	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888699	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888728	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867840	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28649280	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651059	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668628	0.81[EUR][1000 genomes]
rs36189703	0.85[EUR][1000 genomes]
rs4289842	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs56316062	0.81[AFR][1000 genomes]
rs58836328	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59036101	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66883336	0.81[AFR][1000 genomes]
rs67676723	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983626	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7014328	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7014359	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72681699	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7388498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7388507	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7823271	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825662	0.88[ASW][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap]
rs7829098	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7832540	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7837208	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838174	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9693860	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979867	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530386	chr8:117509968-118391406	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv831434	chr8:117784467-117977825	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1027259	chr8:117790928-117842055	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1034015	chr8:117790928-117843979	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7828067	C8orf53	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:117780400-117798800	Weak transcription	HSMMtube	muscle
2	chr8:117780400-117799800	Weak transcription	Fetal Stomach	stomach
3	chr8:117780400-117830200	Weak transcription	Aorta	Aorta
4	chr8:117780600-117796600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr8:117780600-117800600	Weak transcription	Colon Smooth Muscle	Colon
6	chr8:117780600-117800600	Weak transcription	Psoas Muscle	Psoas
7	chr8:117780600-117800800	Weak transcription	Brain Angular Gyrus	brain
8	chr8:117780600-117800800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr8:117780600-117800800	Weak transcription	Brain Substantia Nigra	brain
10	chr8:117780600-117802200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr8:117782000-117814000	Weak transcription	Ovary	ovary
12	chr8:117783400-117796800	Weak transcription	HMEC	breast
13	chr8:117784000-117800600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr8:117784400-117800800	Weak transcription	Fetal Lung	lung
15	chr8:117784600-117800400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr8:117784600-117804800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr8:117784800-117798800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr8:117785400-117800600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr8:117785400-117800800	Weak transcription	Liver	Liver
20	chr8:117785400-117800800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr8:117785400-117801200	Weak transcription	Left Ventricle	heart
22	chr8:117785600-117796600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:117785600-117797200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr8:117785600-117798400	Weak transcription	GM12878-XiMat	blood
25	chr8:117785800-117796200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr8:117785800-117800400	Weak transcription	Dnd41	blood
27	chr8:117786400-117800600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr8:117786400-117800600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr8:117786400-117800600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr8:117786600-117800800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr8:117786600-117800800	Weak transcription	Primary T cells from cord blood	blood
32	chr8:117786600-117800800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr8:117788200-117800800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:117790800-117797400	Weak transcription	HSMM	muscle
35	chr8:117793800-117800800	Weak transcription	Fetal Brain Female	brain
36	chr8:117793800-117800800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr8:117794000-117800400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr8:117794000-117800800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr8:117795000-117796200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr8:117795000-117797400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr8:117795200-117796200	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr8:117795200-117796600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr8:117795200-117796800	Enhancers	H9 Cell Line	embryonic stem cell
44	chr8:117795200-117797600	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr8:117795200-117797600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr8:117795200-117797600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr8:117795400-117796800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr8:117795600-117796400	Enhancers	HepG2	liver
49	chr8:117795600-117797000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr8:117795600-117797200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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